01-22-2009
How can I remove those duplicate sequence in UNIX?What command line I should type?
The input is:
>HWI-EAS382_30FC7AAXX:4:1:1580:1465
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:4:1:1062:1640
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:4:1:272:629
AAAAAAAAGCTATAGTCTCGTCACACATACTCACAA
>HWI-EAS382_30FC7AAXX:4:1:1033:1135
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:4:1:1421:27
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
My desired output is:
>HWI-EAS382_30FC7AAXX:4:1:1580:1465
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:4:1:272:629
AAAAAAAAGCTATAGTCTCGTCACACATACTCACAA
What command line I should type to remove those duplicated sequence?
Thanks for all of your advise.
10 More Discussions You Might Find Interesting
1. UNIX for Dummies Questions & Answers
Hi,
I have a scenario here where I have created a flatfile with the below mentioned information. File as you can see is dispalyed in three columns
1st column is FileNameString
2nd column is Report_Name (this has spaces)
3rd column is Flag
Result file needed is, removal of duplicate... (1 Reply)
Discussion started by: Student37
1 Replies
2. UNIX for Dummies Questions & Answers
Can anyone help me how can i print only the unique entry in a line?
MI_AP MI_AP MI_CM MI_MF
RC_NAP MBS_AP SF_RAN MBS_AP NT_CAR
so that it will on output the one unique entry per line.
MI_AP MI_CM MI_MF
RC_NAP MBS_AP SF_RAN NT_CAR
I can't find the same situation on the knowledge... (5 Replies)
Discussion started by: kharen11
5 Replies
3. Shell Programming and Scripting
My input is listed as:
giNumber RefAminoAcid VarAminoAcid
10190711 P P
10190711 D D
109255248 I A
110349771 A ... (4 Replies)
Discussion started by: patrick chia
4 Replies
4. Shell Programming and Scripting
For example, if I have the file whose content are:
>HWI-EAS382_30FC7AAXX:7:1:927:1368
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:7:1:924:1373
ACGAACTTTAAAGCACCTCTTGGCTCGTATGCCGTC
I want my output calculate the total of nucleotide. So my output should look like this:... (2 Replies)
Discussion started by: patrick chia
2 Replies
5. Shell Programming and Scripting
Hi,
Please help!
I have a file having duplicate words in some line and I want to remove the duplicate words.
The order of the words in the output file doesn't matter.
INPUT_FILE
pink_kite red_pen ball pink_kite ball
yellow_flower white no white no
cloud nine_pen pink cloud pink nine_pen... (6 Replies)
Discussion started by: sam_2921
6 Replies
6. Shell Programming and Scripting
I have a file a.txt having content like
deepak
ram
sham
deepram
sita
kumar
I Want to delete the first line containing "deep" ...
I tried using...
grep -i 'deep' a.txt
It gives me 2 rows...I want to delete the first one..
+ need to know the command to delete the line from... (5 Replies)
Discussion started by: saluja.deepak
5 Replies
7. Shell Programming and Scripting
Hi
Ive been scratching over this for some time with no solution.
I have a file like this
1 bla bla 1
2 bla bla 2
4 bla bla 3
5 bla bla 1
6 bla bla 1
I want to remove consecutive occurrences of lines like bla bla 1, but the first column may be different.
Any ideasss?? (23 Replies)
Discussion started by: jamie_123
23 Replies
8. UNIX for Dummies Questions & Answers
So I have a bunch of files that look like this
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---
>gi|45235353
MMKCR----VEKMRDVFFDESIRWAVQ
They go on...sequences are much longer but all in two line (fasta) format.
I want to remove duplicate pairs of ID(GI) number and sequence. I tried... (12 Replies)
Discussion started by: bakere19
12 Replies
9. Shell Programming and Scripting
Hello,
I have a file which have several duplicate entries on the same line:
File
ID source
1 GM GF GM
2 GM GF GM GF GM GF GM GF GM GF
3 GM GF GM SF GM GF GM SF
4 FF FF FF FF
5 FF GM FF ... (2 Replies)
Discussion started by: nans
2 Replies
10. Shell Programming and Scripting
HI,
I have the below input file
/* ----------------- cmdsDlyStartFWJ -----------------*/
UNIX_JOB CMDS065J
RUN ANY
CMDNAME sleep 5
AGENT CMDSHP
USER proddata
RUN MON,TUE,WED,THU,FRI
DELAYSUB 02:00
/* "Triggers daily file watcher jobs" */
ENVAR... (5 Replies)
Discussion started by: varun22486
5 Replies
uudemon(4) Kernel Interfaces Manual uudemon(4)
NAME
uudemon.admin, uudemon.cleanu, uudemon.hour, uudemon.poll - Administrative shell scripts for polling remote systems, cleaning up spool
directories, reporting status to the system administrator, and routine invocations of the uuxqt and uusched daemons
SYNOPSIS
These shell scripts reside in the following directory:
/usr/lib/uucp
DESCRIPTION
All the scripts can be run from the command line or can be run automatically by the cron daemon. To automatically run the scripts, remove
the comment character (#) from the beginning of the relevant line in the /var/spool/cron/crontabs/uucp file.
This script reports status to the system administrator. It issues the uustat command to find out the status of uucp jobs. It mails the
results to the uucp login ID. The script may be modified to send mail to any login ID such as the uucp administrative login ID (uucpa) or
root. This script cleans up the /var/spool/uucp and /var/spool/uucppublic directories by running the uucleanup command. The uucleanup com-
mand is run with the following parameters: -C7, -D7, X2, -o2, -W1. This script runs the uusched and uuxqt daemons in the background. This
script polls the systems listed in the /usr/lib/uucp/Poll file. The uudemon.poll script should be scheduled before the uudemon.hour
script. This allows uudemon.poll to create any command files before cron runs the uudemon.hour script.
FILES
Contains the uudemon.admin, uudemon.cleanu, uudemon.hour and uudemon.poll files. Contains the uucp file.
RELATED INFORMATION
Commands: cron(8), uucleanup(8), uusched(8), uuxqt(1)
Files: /usr/lib/uucp delim off
uudemon(4)